The purposes of this study were 1) to investigate the heritability, reliability, and selection response for survival traits following a Weibull frailty proportional hazard model; and 2) to examine the relationship between genetic parameters from a Weibull model, a discrete proportional hazard model, and a binary data analysis using a linear model. Both analytical methods and Monte Carlo simulations were used to achieve these aims. Data were simulated using the Weibull frailty model with two different shapes of the Weibull distribution. Breeding values of 100 unrelated sires with 50 to 100 progeny (with different levels of censoring) were generated from a normal distribution and two different sire variances. For analysis of longevity data on the discrete scale, simulated data were transformed to a discrete scale using arbitrary ends of discrete intervals of 400, 800, or 1200 d. For binary data analysis, an individual's longevity was either 0 (when longevity was less than the end of interval) or 1 (when longevity was equal or greater than the end of interval). Three different statistical models were investigated in this study: a Weibull model, a discrete-time model (a proportional hazard model assuming that the survival data are measured on a discrete scale with few classes), and a linear model based upon binary data. An alternative derivation using basic expressions of reliabilities in sire models suggests a simple equation for the heritability on the original scale (effective heritability) that is not dependent on the Weibull parameters. The predictions of reliabilities using the proposed formulae in this study are in very good agreement with reliabilities observed from simulations. In general, the estimates of reliability from either the discrete model or the binary data analysis were close to estimates from the Weibull model for a given number of uncensored records in this simplified case of a balanced design. Although selection response from the binary data analysis depends on the end of interval point, there is a relatively good agreement between selection responses in the Weibull model and the binary data analysis. In general, when the underlying survival data is from a Weibull distribution, it appears that the method of analyzing data does not greatly affect the results in terms of sire ranking or response to selection, at least for the simplified context considered in this study.

The Baluchi breed is the most common native breed of Iran adapted to harsh environments in the eastern parts of the country. The data used in the present study, collected from two research flocks at the Abbasabad sheep breeding station in north-east Iran, included 20 534 animals descended from 363 sires, 5992 dams, 282 maternal grandsires, and 2865 maternal granddams during the period 1966 to 1989. The traits recorded were: birth weight (BW), weaning weight (WW), weight at 6 months (W6), weight at 12 months (YW), pre-weaning gain (WG), postweaning gain (PWG), lamb fleece weight (LFW), ewe fleece weight sheared before first joining (FW1) and adult ewe fleece weight (FW). Genetic parameters, estimated with restricted maximum likelihood and a two-trait animal model, were similar in the two flocks. Direct heritabilities for the various body weight traits were moderate and varied between 0-13 and 0-32, while the maternal heritabilities were low and varied between 0-01 and 0-12. Direct and maternal genetic correlations between WW and weights at later ages were moderate to high (0-59 to 0-96). Direct heritabilities of weight gain measures varied between 0-12 and 0-19, while no significant maternal influence on either of these weight gain measures could be detected. The estimates of direct genetic correlation between WG and PWG were positive and varied between 0-54 and 0-74, while negative maternal genetic correlation (-0-17 on average) between WG and PWG was detected. For LFW, direct heritability was low and no maternal heritability could be shown. For FW1, both direct and maternal genetic influences were demonstrated (0-07 to 0-26). Direct genetic correlation between LFW and FW1 was very low and close to zero, while maternal genetic correlation was positive and relatively high (0-72 on average). The relative contributions to phenotypic variance from variance components due to common environmental effects ranged from 0-01 to 0-15 for all traits. The repeatability of FW was low (0-03 to 0-12).

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A genetic study was carried out to: (1) conduct a genetic analysis of longevity of Swedish Yorkshire sows, (2) study the environmental and genetic factors that influence the presence and severity of osteochondrosis, and (3) investigate the relationship between breeding values for osteochondrosis and longevity of sows. The data for the longevity analyses were extracted from the Swedish litter-recording scheme data bank (Quality Genetics, former Scan Avel HB). After editing original data, records of 9814 Yorkshire sows with 7553 (77%) uncensored and 2261 (23%) censored born 1986 through 1997 were used in the analyses. Litter size at first and last farrowing, age at first farrowing, backfat thickness, daily gain and weight at completion of performance test (~170 days) were included as fixed effects in all analyses. The combination of herd-year effect was treated as fixed or random, time-independent or time-dependent in different analyses. Sire effect was considered as the source of genetic variation and thus a sire model was used. The analyses of osteochondrosis were based on information on 14 388 Landrace and 14 458 Yorkshire pigs from the Swedish pig progeny-testing scheme, recorded from 1987 through 1997. The birth herd and the combination of sex, testing station, year and month for start of test were included as fixed effects in the statistical model. Variance and covariance components for osteochondrosis recorded at elbow and knee joints were estimated in a bivariate animal model by the restricted maximum likelihood method within each breed. In the survival analyses (Yorkshire sows), the fixed effects of herd-year (when it was treated as fixed effect), litter size at first and at last farrowing, age at first farrowing, backfat and gain at completion of performance test were highly significant (P < 0·01). Herd-year combination was the major cause of variation for risk of culling, compared with other fixed effects. The risk of being culled at a certain time decreased as the litter size at first and at last farrowing, or backfat of the gilt at completion of performance test increased. With increasing age at first farrowing, the risk of being culled at a certain time increased. Heritability in the original scale for longevity ranged from 0·21 to 0·31. The results for osteochondrosis showed that the combined effect of sex-testing station-year and month of start of test was highly significant (P < 0·01). Estimates of heritabilities for osteochondrosis score were similar for both Landrace and Yorkshire breeds and was, on average, 0·21. The correlations between breeding values for longevity and osteochondrosis were low (on average 0·07, adjusted for genetic trends) but were significant (P < 0·01) and in a favourable direction: higher osteochondrosis load associated with higher risk of being culled.

The estimation of (co)variance components for multiple traits with maternal genetic effects was found to be influenced by population structure. Two traits in a closed breeding herd with random mating were simulated over nine generations. Population structures were simulated on the basis of different proportions of dams not having performance records (0, 0.1, 0.5, 0.8 and 0.9): three genetic correlations (-0.5, 0.0 and +0.5) between direct and maternal effects and three genetic correlations (0, 0.3 and 0.8) between two traits. Three ratios of direct to maternal genetic variances, (1:3, 1:1, 3:1), were also considered. Variance components were estimated by restricted maximum likelihood. The proportion of dams without records had an effect on the SE of direct-maternal covariance estimates when the proportion was 0.8 or 0.9 and the true correlation between direct and maternal effects was negative. The ratio of direct to maternal genetic variances influenced the SE of the (co)variance estimates more than the proportion of dams with missing records. The correlation between two traits did not have an effect on the SE of the estimates. The proportion of dams without records and the correlation between direct and maternal effects had the strongest effects on bias of estimates. The largest biases were obtained when the proportion of dams without records was high, the correlation between direct and maternal effects was positive, and the direct variance was greater than the maternal variance, as would be the situation for most growth traits in livestock. Total bias in all parameter estimates for two traits was large in the same situations. Poor population structure can affect both bias and SE of estimates of the direct-maternal genetic correlation, and can explain some of the large negative estimates often obtained.

Inclusion of forage and its physical form in starter may affect rumen development, average daily gain (ADG), and dry matter intake (DMI) of dairy calves. To evaluate the effects of forage and its physical form (chopped vs. pelleted) on growth of calves under a high milk feeding regimen, 32 Holstein calves (38.8±1.1kg) were assigned at birth to 1 of 3 treatments in a completely randomized block design. Dietary treatments (% of dry matter) were (1) 100% semi-texturized starter (CON); (2) 90% semi-texturized starter + 10% chopped alfalfa hay (mean particle size=5.4mm) as a total mixed ration (TMR; CH); and (3) 90% semi-texturized starter + 10% pelleted alfalfa (mean=5.8mm) hay as a TMR (PH). Data were subjected to mixed model analysis with contrasts used to evaluate effect of forage inclusion. Calves were weaned at 76 d of age and the experiment finished 2 wk after weaning. Individual milk and solid feed consumption were recorded daily. Solid feed consumption and ADG increased as age increased (effect of week), but neither forage inclusion nor physical form of forage affected these variables pre- or postweaning. Plasma urea N was affected by treatments such that the CON group had a lower concentration than forage-fed groups. Forage inclusion, but not physical form, resulted in increased total protein in plasma. Although days with elevated rectal temperature, fecal score, and general appearance were not affected by dietary treatments, calves fed alfalfa hay during the first month of life had fewer days with respiratory issues, regardless of physical form of hay. We concluded that provision of forage does have some beneficial effects in calves fed large amounts of milk replacer, but pelleted alfalfa hay did not result in any improvement in calf performance or health.

To investigate the effect of heat stress (HS) on production and metabolism of Afshari sheep, 32 intact male lambs (33.2 ± 4.5 kg) were used in a completely randomized design using 2 experimental periods. In period 1 all 32 lambs were housed in thermal neutral (TN) conditions (25.6 ± 2.6°C and a temperature-humidity index [THI] of 72.0 ± 2.6) and fed ad libitum for 8 d. In period 2 (P2; 9 d), 16 lambs were subjected to cyclical HS (29.0 to 43.0°C and a THI ≥80 for 24 h/d) and the other 16 lambs were maintained in TN conditions but pair fed (pair-fed thermal neutral [PFTN]) to the HS lambs. During each period DMI and water intake were measured daily. Respiration rate, rectal temperature, and skin temperature at the shoulder, rump, and front and rear leg were recorded at 0700 and 1400 h daily. Water intake increased (P < 0.05) during P2 in both HS and TN lambs (88 and 35%, respectively). Heat stress increased the 0700 and 1400 h surface temperature at the shoulder (3.0 and 10.6%), rump (2.7 and 12.7%), rear leg (3.1 and 13%), and front leg (3.0 and 13%) and respiratory rates (72 and 124%; P < 0.01, respectively, for 0700 and 1400 h) but only the 1400 h rectal temperature was increased (P < 0.01; 0.54°C) in HS lambs. Plasma glucose concentration decreased in P2 (P < 0.01) in both the HS and PFTN lambs. Basal insulin concentrations decreased in PFTN controls but increased in HS lambs (environment × period interaction; P < 0.05). Blood urea nitrogen concentration was not affected by environment or period, but NEFA levels were slightly elevated (P < 0.01) in both PFTN and HS lambs during P2. Interestingly, HS did not affect DMI, but ADG was reduced (36%; P < 0.01) compared to the PFTN lambs. These results indicate that the direct effects of heat (not mediated by reduced DMI) are partially responsible for reduced growth in heat-stressed lambs.

BackgroundIn aquaculture breeding, resistance against infectious diseases is commonly assessed as time until death under exposure to a pathogen. For some diseases, a fraction of the individuals may appear as "cured" (non-susceptible), and the resulting survival time may thus be a result of two confounded underlying traits, i.e., endurance (individual hazard) and susceptibility (whether at risk or not), which may be accounted for by fitting a cure survival model. We applied a cure model to survival data of Pacific white shrimp (Penaeus vannamei) challenged with the Taura syndrome virus, which is one of the major pathogens of Panaeid shrimp species.MethodsIn total, 15,261 individuals of 513 full-sib families from three generations were challenge-tested in 21 separate tests (tanks). All challenge-tests were run until mortality naturally ceased. Time-until-event data were analyzed with a mixed cure survival model using Gibbs sampling, treating susceptibility and endurance as separate genetic traits.ResultsOverall mortality at the end of test was 28%, while 38% of the population was considered susceptible to the disease. The estimated underlying heritability was high for susceptibility (0.41 ± 0.07), but low for endurance (0.07 ± 0.03). Furthermore, endurance and susceptibility were distinct genetic traits (rg = 0.22 ± 0.25). Estimated breeding values for endurance and susceptibility were only moderately correlated (0.50), while estimated breeding values from classical models for analysis of challenge-test survival (ignoring the cured fraction) were closely correlated with estimated breeding values for susceptibility, but less correlated with estimated breeding values for endurance.ConclusionsFor Taura syndrome resistance, endurance and susceptibility are apparently distinct genetic traits. However, genetic evaluation of susceptibility based on the cure model showed clear associations with standard genetic evaluations that ignore the cure fraction for these data. Using the current testing design, genetic variation in observed survival time and absolute survival at the end of test were most likely dominated by genetic variation in susceptibility. If the aim is to reduce susceptibility, earlier termination of the challenge-test or back-truncation of the follow-up period should be avoided, as this may shift focus of selection towards endurance rather than susceptibility.